Sequence-Dependent Bending of DNA Induced by Cisplatin: NMR Structures of an A⋅T-Rich 14-mer Duplex

Identification by NMR spectroscopy of the two stereoisomers of the platinum complex [PtCl2(S-ahaz)] (S-ahaz = 3(S)-aminohexahydroazepine) bound to a DNA 14-mer oligonucleotide. NMR evidence of structural alteration of a platinated A x T-rich 14-mer DNA duplex

The enantiomers of the asymmetric, chiral platinum(II) complex [PtCl(2)(S-ahaz)] (S-ahaz = 3(S)-aminohexahydroazepine) each form two stereoisomers on binding to GpG sequences of DNA: one in which the primary amine is directed toward the 5' end of the DNA and one in which it is directed toward the 3' end. Previous binding studies have revealed that the S-enantiomer forms the two stereoisomers in a 7:1 ratio while the R-enantiomer forms them in close to a 1:1 ratio. In an attempt to elucidate the reasons behind the stereoselectivity displayed by the S-enantiomer and to establish which isomer is formed in the greater amount, we report here its reaction with a 14-mer oligodeoxyribonucleotide having a single GpG site. The two stereoisomers that formed were separated using HPLC methods, and their integrities were confirmed by electrospray ionization mass spectrometry. The DNA duplex was formed by combination of each of the purified reaction products with the complementary strand of DNA. Identification of both of the stereoisomers was achieved using 2D NMR spectroscopy, which is the first time this has been achieved for an unsymmetric platinum complex bound to DNA. The minor stereoisomer, with the bulk of the ahaz ring directed toward the 3' end of the platinated strand, induced considerable disruption to the 14-mer DNA duplex structure. The primary amine of the ahaz ligand was oriented toward the 3' side of the duplex in the major isomer, giving a DNA structure that was less disrupted and was more akin to the structure of the DNA on binding of cisplatin to the same sequence.

2D NMR study of the DNA duplex d(CTCTC*A*ACTTCC).d(GGAAGTTGAGAG) cross-linked by the antitumor-active dirhodium(II,II) unit at the cytosine-adenine step

The 2D NMR analysis in solution of the DNA duplex d(CTCTC*A*ACTTCC).d(GGAAGTTGAGAG) binding to the dirhodium unit cis-[Rh2(mu-O2CCH3)2(eta1-O2CCH3)]+ showed that an unprecedented intrastrand adduct, dsII, is formed with the dirhodium unit cross-linking in the major groove residues C5 and A6 (indicated with asterisks), also corroborated by enzyme digestion studies. Formation of the dirhodium complex dsII destabilizes significantly the duplex as indicated by the substantial decrease in its melting temperature (DeltaTm = -22.9 degrees C). The reduced thermal stability of dsII is attributed to the decreased stacking of the bases and the complete disruption and/or weakening of the hydrogen bonds within the base pairs in the immediate vicinity of the metalation site (C5.G20 and A6.T19), but the effects due to the metal binding are more severe for the base pairs in the 5' direction to the lesion site. The NMR spectroscopic data indicate that Watson-Crick hydrogen bonding is completely disrupted for the C5.G20 site and considerably weakened for A6.T19. In dsII, the bases C5 and A6 bind to eq positions of the dirhodium unit cis-[Rh2(mu-O2CCH3)2(eta1-O2CCH3)]+, which retains one monodentate and two bridging acetate groups, presumably due to steric reasons. Binding of A6 takes place via N7, whereas binding of the C5 base takes place via the exocyclic N4 site, resulting in the anti-cytosine rotamer with respect to site N3 in its metal-stabilized rare iminooxo form.

Relationship of solution and protein-bound structures of DNA duplexes with the major intrastrand cross-link lesions formed on cisplatin binding to DNA

DNA bases in the three-base-pair (3bp) region of duplexes with the two major lesions of cisplatin (cis-PtCl(2)(NH(3))(2)) with DNA, namely d(XGG) and d(XAG) ( = N7-platinated base), differ in their relative positions by as much as approximately 3.5 A in structures in the literature. Such large differences impede drug design and assessments of the effects of protein binding on DNA structure. One recent and several past structures based on NMR-restrained molecular dynamics (RMD) differ significantly from the reported X-ray structure of an HMG-bound XGG 16-mer DNA duplex (Ohndorf, U.-M.; Rould, M. A.; He, Q.; Pabo, C. O.; Lippard, S. J. Nature 1999, 399, 708). This 16-mer structure has several significant novel and unique features (e.g., a bp step with large positive shift and slide). Hypothesizing that novel structural features in the XGG or XAG region of duplexes elude discovery by NMR methods (especially because of the flexible nature of the 3bp region), we studied an oligomer with only G.C bp's in the XGGY site by NMR methods for the first time. This 9-mer gave a 5'-G N1H signal with a normal shift and intensity and showed clear NOE cross-peaks to C NHb and NHe. We assigned for the first time (13)C NMR signals of a duplex with a GG lesion. These data, by adding NMR-based criteria to those inherent in NOESY and COSY data, have more specifically defined the structural features that should be present in an acceptable model. In particular, our data indicated that the sugar of the X residue has an N pucker and that the GG cross-link should have a structure similar to the original X-ray structure of cis-Pt(NH(3))(2)(d(pGpG)) (Sherman S. E.; Gibson, D.; Wang, A. H.-J.; Lippard, S. J. J. Am. Chem. Soc. 1988, 110, 7368). With these restrictions added to NOE restraints, an acceptable model was obtained only when we started our modeling with the 16-mer structural features. The new X-ray/NMR-based model accounted for the NOESY data better than NOE-based models, was very similar in structure to the 16-mer, and differed from solely NOE-based models. We conclude that all XGG and XAG (X = C or T) duplexes undoubtedly have structures similar to those of the 16-mer and our model. Thus, protein binding does not change greatly the structure of the 3bp region. The structure of this region can now be used in understanding structure-activity relationships needed in the design of new carrier ligands for improving Pt anticancer drug activity.

Slowing of cisplatin aquation in the presence of DNA but not in the presence of phosphate: improved understanding of sequence selectivity and the roles of monoaquated and diaquated species in the binding of cisplatin to DNA

1H-15N HSQC NMR spectroscopy is used to study the aquation reactions of cisplatin in 9 mM NaClO4 and 9 mM phosphate (pH 6) solutions at 298 K. For the first time in a single reaction and, therefore, under a single set of reaction conditions, the amounts of all species formed are followed and the rates of aquation, diaquation, and related anation processes are determined in both media. Binding of phosphate to aquated Pt species is observed, but the initial rate of aquation is not affected by the presence of 9 mM phosphate. The reaction between cisplatin and the 14-base-pair self-complementary oligonucleotide 5'-d(AATTGGTACCAATT)-3', having a GpG intrastrand binding site, is investigated. Various kinetic models for this reaction are evaluated and the most appropriate found to be that with a reversible aquation step and a single binding site for the self-complementary duplex. The rate constant for aquation is (1.62 +/- 0.02) x 10(-5) s-1, with the anation rate constant fixed at 4.6 x 10(-3) M-1 s-1, the value obtained from the aquation studies. The rate constants for monofunctional binding of cis-[PtCl(15NH3)2-(OH2)]+ to the sequence were 0.48 +/- 0.19 and 0.16 +/- 0.06 M-1 s-1 for the 3'- and 5'-guanine bases, respectively. Closure rate constants for the monofunctional adducts are (2.55 +/- 0.07) x 10(-5) and (0.171 +/- 0.011) x 10(-5) s-1, for the 3'- and 5'-guanines, respectively. The presence of DNA slows the aquation of cisplatin by 30-40% compared to that observed in 9 mM NaClO4 or 9 mM phosphate, and there is some evidence that the degree of slowing is sequence dependent. The possibility that cis-[Pt(OH)(NH3)2(OH2)]+ contributes to the binding of cisplatin to DNA is investigated, and it is found that about 1% followed this route, the majority of the binding occurring via the monoaquated species cis-[PtCl(NH3)2(OH2)]+. Comparison of the rates of disappearance of cisplatin in reactions at single defined GpG, ApG, GpA, GpTpG and 1,2-interstrand GG binding sites shows that the adduct profile is determined at the level of monofunctional adduct formation.